221165 2008-05-10 05:47 0000 sci-biology/t-coffee-5.65: stabilization request 2008-07-14 17:02:44 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified All Linux RESOLVED FIXED STABLEREQ P2 normal --- 1 mmokrejs@ribosome.natur.cuni.cz sci-biology@gentoo.org ribosome@gentoo.org mmokrejs@ribosome.natur.cuni.cz 2008-05-10 05:47:51 0000 Please stabilize for x86 and amd64, on May 14 will be a month in the tree. ;-) ribosome@gentoo.org 2008-07-06 21:41:11 0000 Stable on amd64. x86 and ppc: To test, after compiling t-coffee, copy the "sample_seq1.fasta" file from "/usr/share/t-coffee/example" to your home directory. This file contains the amino acid sequences for four homologs of a protein in different species. Run "t_coffee sample_seq1.fasta" to have t-coffee align the sequences, calculate the alignment scores, construct a dendrogram, etc. Output files are created in the working directory. You can check the validity of the calculations by comparing the file "sample_seq1.aln" with the files I am attaching. Both aligments are valid; you will (should) get one or the other depending on your CPU. ribosome@gentoo.org 2008-07-06 21:42:20 0000 Created an attachment (id=159740) Resulting alignment - 1st possibility ribosome@gentoo.org 2008-07-06 21:42:45 0000 Created an attachment (id=159741) Resulting alignment - 2nd possibility fauli@gentoo.org 2008-07-08 05:59:42 0000 x86 stable nixnut@gentoo.org 2008-07-14 17:02:44 0000 ppc stable. closing since we're last. 159740 2008-07-06 21:42 0000 Resulting alignment - 1st possibility sample_seq1.aln-1 text/plain Q0xVU1RBTCBGT1JNQVQgZm9yIFQtQ09GRkVFIFZlcnNpb25fNS42NSBbaHR0cDovL3d3dy50Y29m ZmVlLm9yZ10sIENQVT0wLjA3IHNlYywgU0NPUkU9MzMsIE5zZXE9NCwgTGVuPTgxIAoKaG1nbF90 cnliciAgICAgIGtrZHNuYXBrcmFtdHNmbWZmc3NkZnJza2hzZGxzLS0tLS1pdmVtc2thYWdhYXdr ZWxncGVlcmt2eWVlbQpobWd0X21vdXNlICAgICAgLS0tLS1rcGtycHJzYXluaXl2c2VzZnFlYWtk ZHMtLS0tLWFxZ2tsa2x2bmVhd2tubHNwZWVrcWF5aXFsCmhtZ2JfY2hpdGUgICAgICAtLS1hZGtw a3JwbHNheW1sd2xuc2FyZXNpa3JlbnBkZmstdnRldmFra2dnZWx3cmdsa2QtLWtzZXdlYWsKaG1n bF93aGVhdCAgICAgIC0tZHBua3BrcmFwc2FmZnZmbWdlZnJlZWZrcWtucGtua3N2YWF2Z2thYWdl cndrc2xzZXNla2FweXZhawogICAgICAgICAgICAgICAgICAgICAgKioqLiA6OjogLjogLi4gIC4u IC4gIC4gICAgICAgICAgKiAgLiAgKjogKiAgICA6ICA6ICAgCgpobWdsX3RyeWJyICAgICAgYWVr ZGtlcnlrcmVtLS0tLS0tLS0tCmhtZ3RfbW91c2UgICAgICBha2RkcmlyeWRuZW1rc3dlZXFtYWUK aG1nYl9jaGl0ZSAgICAgIGFhdGFrcW55aXJhbHFleWVybi1nZwpobWdsX3doZWF0ICAgICAgYW5r bGtnZXlua2FpYWF5bmtnZXNhCiAgICAgICAgICAgICAgICAqICAgOiAuKiAuIDogICAgICAgICAK CgoK 159741 2008-07-06 21:42 0000 Resulting alignment - 2nd possibility sample_seq1.aln-2 text/plain Q0xVU1RBTCBGT1JNQVQgZm9yIFQtQ09GRkVFIFZlcnNpb25fNS42NSBbaHR0cDovL3d3dy50Y29m ZmVlLm9yZ10sIENQVT0wLjA2IHNlYywgU0NPUkU9MzQsIE5zZXE9NCwgTGVuPTgxIAoKaG1nYl9j aGl0ZSAgICAgIC0tLWFka3BrcnBsc2F5bWx3bG5zYXJlc2lrcmVucGRmay12dGV2YWtrZ2dlbHdy Z2xrZC0ta3Nld2VhawpobWdsX3RyeWJyICAgICAga2tkc25hcGtyYW10c2ZtZmZzc2RmcnNraHMt LS0tLWRsc2l2ZW1za2FhZ2Fhd2tlbGdwZWVya3Z5ZWVtCmhtZ2xfd2hlYXQgICAgICAtLWRwbmtw a3JhcHNhZmZ2Zm1nZWZyZWVma3FrbnBrbmtzdmFhdmdrYWFnZXJ3a3Nsc2VzZWthcHl2YWsKaG1n dF9tb3VzZSAgICAgIC0tLS0ta3BrcnByc2F5bml5dnNlc2ZxZWFrZGRzYXFna2wtLS0tLWtsdm5l YXdrbmxzcGVla3FheWlxbAogICAgICAgICAgICAgICAgICAgICAgKioqLiA6OjogLjogLi4gIC4u IC4gICAgICAgICAgICAgKiAgLiAgKjogKiAgICA6ICA6ICAgCgpobWdiX2NoaXRlICAgICAgYWF0 YWtxbnlpcmFscWV5ZXJuLWdnCmhtZ2xfdHJ5YnIgICAgICBhZWtka2VyeWtyZW0tLS0tLS0tLS0K aG1nbF93aGVhdCAgICAgIGFua2xrZ2V5bmthaWFheW5rZ2VzYQpobWd0X21vdXNlICAgICAgYWtk ZHJpcnlkbmVta3N3ZWVxbWFlCiAgICAgICAgICAgICAgICAqICAgOiAuKiAuIDogICAgICAgICAK CgoK